manta_isec: Intersect two Manta VCF files

In pdiakumis/woofr: Helper R Functions for woof

Intersect two Manta VCF files

Description

Intersects two Manta VCF files for evaluation.

Usage

manta_isec(f1, f2, samplename, flab, bnd_switch = TRUE)

Arguments

f1	Path to first Manta file
f2	Path to second ('truthset') Manta file
samplename	Sample name (used for labelling).
flab	File name (used for labelling).
bnd_switch	Logical. Switch BND pairs for more matches (default: TRUE).

Value

A list with the following elements:

• tot_vars: total variants for file1 and file2

• fp: tibble with False Positive calls i.e. variants in f1 that are not in f2

• fn: tibble with False Negative calls i.e. variants in f2 that are not in f1

Examples

## Not run: 
f1 <- "path/to/run1/manta.vcf.gz"
f2 <- "path/to/run2/manta.vcf.gz"
mi <- manta_isec(f1, f2)

## End(Not run)

pdiakumis/woofr documentation built on Jan. 4, 2024, 11:22 a.m.